22 pre publish code tidy

.devcontainer/Dockerfile

@@ -9,7 +9,7 @@ RUN apt-get install -y \
 
 # Packages for local testing
 RUN pip install --upgrade pip setuptools wheel
-RUN pip install pytest h5py numpy
+RUN pip install pytest numpy
 
 # Packages for local build
 RUN pip install cmake ninja
@@ -25,5 +25,4 @@ RUN apt-get install -y \
 RUN apt-get install -y \
     python3-dev \
     libboost-dev \
-    libeigen3-dev \
     pybind11-dev

.github/workflows/build-cpp-libs.yml

@@ -19,16 +19,16 @@ jobs:
         include:
           - os: ubuntu-22.04
             build-type: Debug
-            system-deps: "sudo apt -y install libboost-dev libboost-math-dev libeigen3-dev"
+            system-deps: "sudo apt -y install libboost-dev libboost-math-dev"
           - os: ubuntu-22.04
             build-type: Release
-            system-deps: "sudo apt -y install libboost-dev libboost-math-dev libeigen3-dev"
+            system-deps: "sudo apt -y install libboost-dev libboost-math-dev"
           - os: macos-14
             build-type: Debug
-            system-deps: "brew install boost eigen"
+            system-deps: "brew install boost"
           - os: macos-14
             build-type: Release
-            system-deps: "brew install boost eigen"
+            system-deps: "brew install boost"
 
     steps:
 

.github/workflows/build-wheels.yml

@@ -27,12 +27,12 @@ jobs:
           - os: macos-13
             arch: x86_64
             py-vers: cp38-* cp39-* cp310-* cp311-* cp312-*
-            before-all: brew install cmake ninja boost eigen
+            before-all: brew install cmake ninja boost
             extra-env: CC="$(brew --prefix llvm@15)/bin/clang" CXX="$(brew --prefix llvm@15)/bin/clang++" HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1
           - os: macos-14
             arch: arm64
             py-vers: cp39-* cp310-* cp311-* cp312-*
-            before-all: brew install cmake ninja boost eigen
+            before-all: brew install cmake ninja boost
             extra-env: CC="$(brew --prefix llvm@15)/bin/clang" CXX="$(brew --prefix llvm@15)/bin/clang++" HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1
 
     env:

.github/workflows/ctest-macos.yml

@@ -16,7 +16,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: install system packages
-        run: brew install boost eigen
+        run: brew install boost
 
       - name: make build directory
         run: mkdir build_dir

.github/workflows/ctest-ubuntu.yml

@@ -21,7 +21,7 @@ jobs:
       - name: install system packages
         run: |
           sudo apt -y update
-          sudo apt -y install libboost-dev libeigen3-dev
+          sudo apt -y install libboost-dev
 
       - name: make build directory
         run: mkdir build_dir

.github/workflows/pytest-ubuntu.yml

@@ -38,7 +38,7 @@ jobs:
       - name: install system packages
         run: |
           sudo apt -y update
-          sudo apt -y install libboost-dev libeigen3-dev
+          sudo apt -y install libboost-dev
 
       - name: install python dependencies
         run: |

.vscode/settings.json

@@ -7,7 +7,85 @@
     "cmake.generator": "Ninja",
     "cmake.configureOnOpen": false,
     "cmake.configureSettings": {
-        //"ENABLE_TESTING": "ON",
-        //"WARNINGS_AS_ERRORS": "TRUE",
+        "ENABLE_TESTING": "ON",
+        "WARNINGS_AS_ERRORS": "TRUE"
+    },
+    "files.associations": {
+        "iosfwd": "cpp",
+        "cctype": "cpp",
+        "clocale": "cpp",
+        "cmath": "cpp",
+        "csignal": "cpp",
+        "cstdarg": "cpp",
+        "cstddef": "cpp",
+        "cstdio": "cpp",
+        "cstdlib": "cpp",
+        "cstring": "cpp",
+        "ctime": "cpp",
+        "cwchar": "cpp",
+        "cwctype": "cpp",
+        "array": "cpp",
+        "atomic": "cpp",
+        "strstream": "cpp",
+        "bit": "cpp",
+        "*.tcc": "cpp",
+        "bitset": "cpp",
+        "chrono": "cpp",
+        "codecvt": "cpp",
+        "compare": "cpp",
+        "complex": "cpp",
+        "concepts": "cpp",
+        "condition_variable": "cpp",
+        "cstdint": "cpp",
+        "deque": "cpp",
+        "forward_list": "cpp",
+        "list": "cpp",
+        "map": "cpp",
+        "set": "cpp",
+        "string": "cpp",
+        "unordered_map": "cpp",
+        "unordered_set": "cpp",
+        "vector": "cpp",
+        "exception": "cpp",
+        "algorithm": "cpp",
+        "functional": "cpp",
+        "iterator": "cpp",
+        "memory": "cpp",
+        "memory_resource": "cpp",
+        "numeric": "cpp",
+        "optional": "cpp",
+        "random": "cpp",
+        "ratio": "cpp",
+        "regex": "cpp",
+        "string_view": "cpp",
+        "system_error": "cpp",
+        "tuple": "cpp",
+        "type_traits": "cpp",
+        "utility": "cpp",
+        "fstream": "cpp",
+        "future": "cpp",
+        "initializer_list": "cpp",
+        "iomanip": "cpp",
+        "iostream": "cpp",
+        "istream": "cpp",
+        "limits": "cpp",
+        "mutex": "cpp",
+        "new": "cpp",
+        "numbers": "cpp",
+        "ostream": "cpp",
+        "semaphore": "cpp",
+        "sstream": "cpp",
+        "stdexcept": "cpp",
+        "stop_token": "cpp",
+        "streambuf": "cpp",
+        "thread": "cpp",
+        "cfenv": "cpp",
+        "cinttypes": "cpp",
+        "typeindex": "cpp",
+        "typeinfo": "cpp",
+        "valarray": "cpp",
+        "variant": "cpp",
+        "core": "cpp",
+        "geometry": "cpp"
     }
 }

CMakeLists.txt

@@ -1,5 +1,18 @@
-# This file is part of https://github.com/PalamaraLab/threads which is released under the GPL-3.0 license.
-# See accompanying LICENSE and COPYING for copyright notice and full details.
+# This file is part of the Threads software suite.
+# Copyright (C) 2024 Threads Developers.
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 cmake_minimum_required(VERSION 3.16)
 message(STATUS "Using CMake version ${CMAKE_VERSION}")
@@ -16,9 +29,7 @@ include(cmake/ProjectSettings.cmake)
 # Link this 'library' to use the warnings specified in CompilerWarnings.cmake
 add_library(project_warnings INTERFACE)
 include(cmake/CompilerWarnings.cmake)
-
-# FIXME Uncomment to enable warnings
-#set_project_warnings(project_warnings)
+set_project_warnings(project_warnings)
 
 # Sanitiser options if supported by compiler
 include(cmake/Sanitisers.cmake)